bio-commandeer 0.0.1 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -28,6 +28,24 @@ Of course, when running commands such as this, take care not to trust the input
 
 Note: this software is under active development! Currently it is perhaps overly opinionated and as such not overly flexible.
 
+## Logging
+Commands run are logged with level info, if requested:
+```ruby
+require 'bio-commandeer'
+Bio::Log::CLI.logger("stderr"); Bio::Log::CLI.trace("info");
+puts Bio::Commandeer.run 'echo 5', :log=>true
+```
+On stderr this gives
+```
+ INFO bio-commandeer: Running command: echo 5\n"+
+ INFO bio-commandeer: Command finished with exitstatus 0"
+```
+Or a logging can be given directly, so long as it has an `info` method:
+```ruby
+Bio::Commandeer.run 'echo 5', :log=>my_logger
+```
+
+
 ## Installation
 
 ```sh

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.1.0

data/lib/bio-commandeer.rb

@@ -1,14 +1,4 @@
 
-
 require 'bio-logger'
-Bio::Log::LoggerPlus.new('bio-commandeer')
-module Bio
-  module CommandeerLogging
-    def log
-      Bio::Log::LoggerPlus['bio-commandeer']
-    end
-  end
-end
-
 
 require 'bio-commandeer/commandeer.rb'

data/lib/bio-commandeer/commandeer.rb

@@ -3,21 +3,24 @@ require 'systemu'
 module Bio
   # See #run
   class Commandeer
-    include Bio::CommandeerLogging
 
     # Run a command line program, and be opinionated about how to handle failure
     #
     # command is a string of the command to be run
     # * options is a hash, with keys:
     # :stdin: a string that is the stdin
-    # :log: turn on logging
+    # :log: if true, turn on logging. If given an object use it as the logger
     def self.run(command, options={})
       if options[:log]
-        log_name = 'bio-commandeer'
-        @log = Bio::Log::LoggerPlus[log_name]
-        if @log.nil? or @log.outputters.empty?
-          @log = Bio::Log::LoggerPlus.new(log_name)
-          Bio::Log::CLI.configure(log_name)
+        if options[:log] == true
+          log_name = 'bio-commandeer'
+          @log = Bio::Log::LoggerPlus[log_name]
+          if @log.nil? or @log.outputters.empty?
+            @log = Bio::Log::LoggerPlus.new(log_name)
+            Bio::Log::CLI.configure(log_name)
+          end
+        else
+          @log = options[:log]
         end
 
         @log.info "Running command: #{command}"

data/spec/bio-commandeer_spec.rb

@@ -1,4 +1,5 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'tempfile'
 
 describe "BioCommandeer" do
   it "should return stdout" do
@@ -8,4 +9,46 @@ describe "BioCommandeer" do
   it 'should raise when exit status the command fails' do
     expect {Bio::Commandeer.run("cat /definitelyNotAFile")}.to raise_error
   end
+
+  it 'should accept stdin' do
+    Bio::Commandeer.run('cat', :stdin => 'dog').should == "dog"
+  end
+
+  it 'should do logging with bio-logger' do
+    Tempfile.open('script') do |f|
+      f.puts [
+        "require 'bio-commandeer'",
+        'Bio::Log::CLI.logger("stderr"); Bio::Log::CLI.trace("info")',
+        "puts Bio::Commandeer.run 'echo 5', :log=>true"
+      ].join("\n")
+      f.close
+      lib = File.join(File.dirname(__FILE__), '..', 'lib')
+
+      status, stdout, stderr = systemu "RUBYLIB=$RUBYLIB:#{lib} ruby #{f.path}"
+
+      stderr.should == " INFO bio-commandeer: Running command: echo 5\n"+
+        " INFO bio-commandeer: Command finished with exitstatus 0\n"
+      stdout.should == "5\n"
+    end
+  end
+
+  it 'should do logging given a log object' do
+    Tempfile.open('script') do |f|
+      f.puts [
+        "require 'bio-commandeer'",
+        'Bio::Log::CLI.logger("stderr"); Bio::Log::CLI.trace("info")',
+        'log = Bio::Log::LoggerPlus.new("anotherlog"); Bio::Log::CLI.configure("anotherlog")',
+        "puts Bio::Commandeer.run 'echo 50', :log=>log"
+      ].join("\n")
+      f.close
+      lib = File.join(File.dirname(__FILE__), '..', 'lib')
+
+      status, stdout, stderr = systemu "RUBYLIB=$RUBYLIB:#{lib} ruby #{f.path}"
+
+      # Note the source of the log
+      stderr.should == " INFO anotherlog: Running command: echo 50\n"+
+        " INFO anotherlog: Command finished with exitstatus 0\n"
+      stdout.should == "50\n"
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-commandeer
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.1.0
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-12 00:00:00.000000000 Z
+date: 2014-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger